Imputation Report For Cohort: C58_cohort

Per chromosome imputation report for cohort C58_cohort.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 12.4.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 12989316 73.862
0.1 1220278 6.939
0.2 810374 4.608
0.3 619465 3.523
0.4 495044 2.815
0.5 404896 2.302
0.6 348948 1.984
0.7 290824 1.654
0.8 240831 1.369
0.9 165960 0.944
Total 17585936 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.3 878178 4.994
0.4 986205 5.608
0.5 1266433 7.201
0.6 1745532 9.926
0.7 2316549 13.173
0.8 2866924 16.302
0.9 7473260 42.496
1.0 52855 0.301
Total 17585936 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 986394 74.2386
0.1 90432 6.8062
0.2 57825 4.3521
0.3 45498 3.4243
0.4 37184 2.7986
0.5 30231 2.2753
0.6 27317 2.0560
0.7 21929 1.6504
0.8 18651 1.4037
0.9 13219 0.9949
Total 1328680

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 67228 5.0598
0.4 75101 5.6523
0.5 96921 7.2945
0.6 133319 10.0339
0.7 179751 13.5285
0.8 219483 16.5189
0.9 552893 41.6122
1.0 3984 0.2998
Total 1328680

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1105124 74.6808
0.1 101200 6.8388
0.2 65193 4.4055
0.3 49964 3.3764
0.4 39061 2.6396
0.5 32681 2.2085
0.6 28663 1.9370
0.7 23142 1.5639
0.8 20272 1.3699
0.9 14497 0.9797
Total 1479797

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 68964 4.6604
0.4 77064 5.2077
0.5 99543 6.7268
0.6 142105 9.6030
0.7 195576 13.2164
0.8 242376 16.3790
0.9 649661 43.9020
1.0 4508 0.3046
Total 1479797

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 915800 73.9198
0.1 87495 7.0623
0.2 55668 4.4933
0.3 42477 3.4286
0.4 35295 2.8489
0.5 29045 2.3444
0.6 24752 1.9979
0.7 20362 1.6435
0.8 16625 1.3419
0.9 11392 0.9195
Total 1238911

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 56462 4.5574
0.4 62799 5.0689
0.5 83462 6.7367
0.6 119177 9.6195
0.7 162192 13.0915
0.8 205301 16.5711
0.9 546140 44.0823
1.0 3378 0.2727
Total 1238911

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 899611 73.2200
0.1 81623 6.6434
0.2 61054 4.9692
0.3 45890 3.7350
0.4 32970 2.6835
0.5 27692 2.2539
0.6 24465 1.9912
0.7 21592 1.7574
0.8 19906 1.6202
0.9 13838 1.1263
Total 1228641

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 56355 4.5868
0.4 63463 5.1653
0.5 82698 6.7309
0.6 118447 9.6405
0.7 159639 12.9931
0.8 200990 16.3587
0.9 543008 44.1958
1.0 4041 0.3289
Total 1228641

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 838247 74.1976
0.1 76469 6.7687
0.2 52586 4.6547
0.3 40412 3.5771
0.4 31572 2.7946
0.5 25058 2.2180
0.6 22023 1.9494
0.7 18234 1.6140
0.8 14947 1.3230
0.9 10202 0.9030
Total 1129750

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 52095 4.6112
0.4 56869 5.0338
0.5 73670 6.5209
0.6 104981 9.2924
0.7 146100 12.9321
0.8 182520 16.1558
0.9 509734 45.1192
1.0 3781 0.3347
Total 1129750

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 820483 73.3437
0.1 81743 7.3071
0.2 53221 4.7575
0.3 40093 3.5839
0.4 32568 2.9113
0.5 26248 2.3463
0.6 22229 1.9871
0.7 17244 1.5415
0.8 15082 1.3482
0.9 9771 0.8734
Total 1118682

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 46574 4.1633
0.4 51520 4.6054
0.5 66963 5.9859
0.6 97798 8.7423
0.7 136853 12.2334
0.8 177917 15.9042
0.9 536814 47.9863
1.0 4243 0.3793
Total 1118682

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 734353 73.8108
0.1 68392 6.8742
0.2 47912 4.8157
0.3 35464 3.5645
0.4 28995 2.9143
0.5 22765 2.2881
0.6 19592 1.9692
0.7 16384 1.6468
0.8 12193 1.2255
0.9 8862 0.8907
Total 994912

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 48675 4.8924
0.4 55316 5.5599
0.5 71153 7.1517
0.6 97372 9.7870
0.7 131513 13.2186
0.8 163194 16.4029
0.9 424660 42.6832
1.0 3029 0.3044
Total 994912

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 734130 74.8050
0.1 64590 6.5815
0.2 44322 4.5162
0.3 32103 3.2712
0.4 27834 2.8362
0.5 21463 2.1870
0.6 19264 1.9629
0.7 15431 1.5724
0.8 13291 1.3543
0.9 8964 0.9134
Total 981392

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 46657 4.7542
0.4 50100 5.1050
0.5 64053 6.5267
0.6 89582 9.1281
0.7 125687 12.8070
0.8 160138 16.3174
0.9 441681 45.0056
1.0 3494 0.3560
Total 981392

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 549040 74.1109
0.1 53660 7.2432
0.2 33824 4.5657
0.3 24869 3.3569
0.4 20426 2.7572
0.5 15830 2.1368
0.6 14587 1.9690
0.7 11508 1.5534
0.8 9733 1.3138
0.9 7359 0.9933
Total 740836

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 33751 4.5558
0.4 38437 5.1883
0.5 49310 6.6560
0.6 71244 9.6167
0.7 96990 13.0920
0.8 125133 16.8908
0.9 323692 43.6928
1.0 2279 0.3076
Total 740836

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 640299 73.8074
0.1 60590 6.9842
0.2 40007 4.6116
0.3 28830 3.3232
0.4 24549 2.8298
0.5 21032 2.4244
0.6 16985 1.9579
0.7 14019 1.6160
0.8 12634 1.4563
0.9 8582 0.9892
Total 867527

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 38225 4.4062
0.4 41827 4.8214
0.5 54270 6.2557
0.6 77626 8.9480
0.7 110188 12.7014
0.8 141187 16.2747
0.9 400902 46.2120
1.0 3302 0.3806
Total 867527

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 637097 73.8688
0.1 59299 6.8755
0.2 36089 4.1844
0.3 31350 3.6349
0.4 24172 2.8026
0.5 20571 2.3851
0.6 17941 2.0802
0.7 14654 1.6991
0.8 12104 1.4034
0.9 9194 1.0660
Total 862471

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 39297 4.5563
0.4 43955 5.0964
0.5 58881 6.8270
0.6 83303 9.6586
0.7 111944 12.9795
0.8 138611 16.0714
0.9 383120 44.4212
1.0 3360 0.3896
Total 862471

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 608619 74.0255
0.1 56144 6.8287
0.2 35865 4.3622
0.3 30535 3.7139
0.4 22842 2.7782
0.5 19023 2.3137
0.6 15965 1.9418
0.7 12754 1.5513
0.8 12144 1.4771
0.9 8284 1.0076
Total 822175

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 38966 4.7394
0.4 43151 5.2484
0.5 54424 6.6195
0.6 78149 9.5052
0.7 106316 12.9311
0.8 133715 16.2636
0.9 364365 44.3172
1.0 3089 0.3757
Total 822175

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 447875 72.6822
0.1 42894 6.9609
0.2 27927 4.5321
0.3 22725 3.6879
0.4 17572 2.8516
0.5 15582 2.5287
0.6 12357 2.0053
0.7 11510 1.8679
0.8 9702 1.5745
0.9 8066 1.3090
Total 616210

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 26665 4.3273
0.4 29732 4.8250
0.5 39135 6.3509
0.6 57535 9.3369
0.7 81419 13.2129
0.8 102499 16.6338
0.9 277374 45.0129
1.0 1851 0.3004
Total 616210

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 411335 74.1691
0.1 38932 7.0199
0.2 25809 4.6537
0.3 18632 3.3596
0.4 15214 2.7433
0.5 11798 2.1273
0.6 10149 1.8300
0.7 8974 1.6181
0.8 7931 1.4301
0.9 5817 1.0489
Total 554591

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 26757 4.8246
0.4 31134 5.6139
0.5 40126 7.2352
0.6 55908 10.0809
0.7 73530 13.2584
0.8 90195 16.2633
0.9 235585 42.4791
1.0 1356 0.2445
Total 554591

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 359555 73.8675
0.1 33501 6.8825
0.2 22036 4.5271
0.3 16902 3.4724
0.4 14245 2.9265
0.5 11855 2.4355
0.6 8931 1.8348
0.7 7894 1.6218
0.8 6540 1.3436
0.9 5298 1.0884
Total 486757

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 25315 5.2007
0.4 29390 6.0379
0.5 37672 7.7394
0.6 51238 10.5264
0.7 66441 13.6497
0.8 80703 16.5797
0.9 195061 40.0736
1.0 937 0.1925
Total 486757

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 386348 73.9108
0.1 37568 7.1870
0.2 22742 4.3507
0.3 19133 3.6603
0.4 14402 2.7552
0.5 11934 2.2830
0.6 10809 2.0678
0.7 9383 1.7950
0.8 6355 1.2158
0.9 4048 0.7744
Total 522722

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 30214 5.7801
0.4 33987 6.5019
0.5 42614 8.1523
0.6 57234 10.9492
0.7 72563 13.8818
0.8 88743 16.9771
0.9 196357 37.5643
1.0 1010 0.1932
Total 522722

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 324184 73.2813
0.1 30216 6.8303
0.2 22791 5.1519
0.3 15592 3.5245
0.4 13546 3.0621
0.5 11043 2.4963
0.6 9038 2.0430
0.7 7830 1.7700
0.8 5609 1.2679
0.9 2534 0.5728
Total 442383

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 32804 7.4153
0.4 36722 8.3010
0.5 46096 10.4199
0.6 54933 12.4175
0.7 63323 14.3141
0.8 71600 16.1851
0.9 136104 30.7661
1.0 801 0.1811
Total 442383

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 356306 73.3741
0.1 33896 6.9802
0.2 23587 4.8573
0.3 17667 3.6382
0.4 13960 2.8748
0.5 10918 2.2483
0.6 9458 1.9477
0.7 8078 1.6635
0.8 6605 1.3602
0.9 5127 1.0558
Total 485602

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 23576 4.8550
0.4 27000 5.5601
0.5 36697 7.5570
0.6 50731 10.4470
0.7 66687 13.7329
0.8 79666 16.4056
0.9 199973 41.1804
1.0 1272 0.2619
Total 485602

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 237780 71.4170
0.1 28359 8.5176
0.2 18465 5.5459
0.3 12823 3.8514
0.4 9688 2.9098
0.5 8179 2.4566
0.6 6623 1.9892
0.7 5599 1.6817
0.8 3731 1.1206
0.9 1699 0.5103
Total 332946

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 31189 9.3676
0.4 35471 10.6537
0.5 40058 12.0314
0.6 44010 13.2184
0.7 46341 13.9185
0.8 51010 15.3208
0.9 84529 25.3882
1.0 338 0.1015
Total 332946

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 280531 73.7578
0.1 26934 7.0815
0.2 18027 4.7397
0.3 13416 3.5274
0.4 11200 2.9447
0.5 8919 2.3450
0.6 7797 2.0500
0.7 5990 1.5749
0.8 4472 1.1758
0.9 3055 0.8032
Total 380341

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 20065 5.2755
0.4 23250 6.1129
0.5 31213 8.2066
0.6 43029 11.3133
0.7 52372 13.7697
0.8 61692 16.2202
0.9 147801 38.8601
1.0 919 0.2416
Total 380341

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 162735 71.9773
0.1 15954 7.0564
0.2 10228 4.5238
0.3 8986 3.9745
0.4 7157 3.1655
0.5 5947 2.6303
0.6 4930 2.1805
0.7 4447 1.9669
0.8 4010 1.7736
0.9 1698 0.7510
Total 226092

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 12746 5.6375
0.4 14374 6.3576
0.5 19242 8.5107
0.6 25396 11.2326
0.7 30617 13.5418
0.8 36468 16.1297
0.9 86720 38.3561
1.0 529 0.2340
Total 226092

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 165097 73.4698
0.1 15983 7.1126
0.2 11003 4.8964
0.3 7819 3.4795
0.4 7010 3.1195
0.5 5253 2.3376
0.6 4657 2.0724
0.7 4013 1.7858
0.8 2553 1.1361
0.9 1326 0.5901
Total 224714

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 14815 6.5928
0.4 17220 7.6631
0.5 21614 9.6184
0.6 27429 12.2062
0.7 31687 14.1010
0.8 36159 16.0911
0.9 75353 33.5328
1.0 437 0.1945
Total 224714

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 388373 74.7153
0.1 34404 6.6186
0.2 24193 4.6543
0.3 18285 3.5177
0.4 13582 2.6129
0.5 11829 2.2757
0.6 10416 2.0038
0.7 9853 1.8955
0.8 5741 1.1045
0.9 3128 0.6018
Total 519804

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 40783 7.8458
0.4 48323 9.2964
0.5 56618 10.8922
0.6 64986 12.5020
0.7 68820 13.2396
0.8 77624 14.9333
0.9 161733 31.1142
1.0 917 0.1764
Total 519804

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering